feat: Python interfaces to geos from Makutu repo

pygeos-tools/pyproject.toml

@@ -22,6 +22,10 @@ dependencies = [
     "numpy",
     "scipy",
     "mpi4py",
+    "vtk",
+    "pyevtk",
+    "xmltodict",
+    "h5py",
 ]
 
 [tool.mypy]

pygeos-tools/src/geos/pygeos_tools/utilities/input/GeosxArgs.py

@@ -0,0 +1,202 @@
+# ------------------------------------------------------------------------------------------------------------
+# SPDX-License-Identifier: LGPL-2.1-only
+#
+# Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
+# Copyright (c) 2018-2024 TotalEnergies
+# Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
+# Copyright (c) 2023-2024 Chevron
+# Copyright (c) 2019-     GEOS/GEOSX Contributors
+# Copyright (c) 2019-     INRIA project-team Makutu 
+# All rights reserved
+#
+# See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+# ------------------------------------------------------------------------------------------------------------
+
+import sys
+import argparse
+
+class GeosxArgs:
+    """ 
+    Class containing the main argument in command line for GEOSX
+
+    Attributes
+    ----------
+        cmdline : list of str
+            List corresponding to a splitted GEOSX submission line
+        options : dict
+            Dict containing GEOSX main options
+    """
+    def __init__(self, args=sys.argv.copy()):
+        """
+        Parameters
+        ----------
+            args : list of str
+                List corresponding to a splitted submission line with options
+        """
+        self.cmdline = args
+        self.options = self.optionsParser()
+
+
+    def optionsParser(self, cmdline=[]):
+        """
+        Return a dict with useful geosx options parsed from a list/submission line.
+
+        Parameters
+        ----------
+            cmdline : list of str
+                List corresponding to a splitted GEOSX submission line          
+
+        Returns
+        --------
+            dict : 
+                Dict containing GEOSX main options
+        """
+        if not cmdline:
+            cmdline = self.cmdline
+        desc = "Parser of GEOSX command line"
+        parser = argparse.ArgumentParser("GEOSX command line parser",
+                                        allow_abbrev=False,
+                                        description=desc)
+
+        parser.add_argument("--input", "-i", "--xml",
+                            type=str, dest="xml", default=None, 
+                            help="XML input file")
+        parser.add_argument("--restart", "-r",
+                            dest="restart", type=str, default=None,
+                            help="Target restart filename")
+        parser.add_argument("-x-partitions", "-x",
+                            type=int, dest="xpart", default=None,
+                            help="Number of partitions in the x direction.")
+        parser.add_argument("-y-partitions", "-y",
+                            type=int, dest="ypart", default=None,
+                            help="Number of partitions in the y direction.")
+        parser.add_argument("-z-partitions", "-z",
+                            type=int, dest="zpart", default=None,
+                            help="Number of partitions in the z direction.")
+        parser.add_argument("--output", "-o",
+                            type=str, dest="outputdir", default=None,
+                            help="Directory to put the output files")
+        parser.add_argument("--use-nonblocking", "-b", default=None,
+                            dest="non_blocking", action="store_true",
+                            help="Use non-blocking MPI communication")
+        parser.add_argument("--name", "-n",
+                            dest="name", default=None,
+                            help="Name of the problem, used for output")
+        parser.add_argument("--suppress-pinned", "-s",
+                            dest="supp_pinned", action="store_true", default=None,
+                            help="Suppress usage of pinned memory for MPI communication buffers")
+        parser.add_argument("--timers", "-t",
+                            type=str, dest="timers", default=None,
+                            help="String specifying the type of timer output")
+        parser.add_argument("--trace-data-migration",
+                            dest="trace_data_mig", action="store_true", default=None,
+                            help="Trace host-device data migration")
+        parser.add_argument("--pause-for", 
+                            dest="pause_for", default=None,
+                            help="Pause geosx for a given number of seconds before starting execution")
+
+        return vars(parser.parse_known_args(cmdline)[0])
+
+
+    def updateArg(self, optionName=None, newValue=None):
+        """
+        Update the GEOSX initialization arguments
+
+        Parameters
+        ----------
+            optionName : str
+                Name of the option to update
+            newValue : str
+                New value for the argument to be updated.
+
+        Returns
+        -------
+            bool : True if the option has been (found and) updated. False otherwise.
+        """
+        if optionName is not None:
+            if self.options[optionName] != newValue:
+                self.options.update({optionName: newValue})
+                return True
+
+        return False
+
+
+    def getCommandLine(self):
+        """
+        Return the command line specific to GEOSX initialization
+
+        Returns
+        --------
+            cl : list of str
+                List containing all the options requested
+        """
+        cl = [""]
+        for opt, val in self.options.items():
+            if val is not None:
+                ab = GeosxAbbrevOption().getAbbrv(opt)
+                cl += [ab]
+                if not isinstance(self.options[opt], bool):
+                   cl += [str(self.options[opt])]
+
+        return cl
+
+
+class GeosxAbbrevOption:
+    """
+    Class containing GEOSX command line options abbreviations
+
+    Attributes
+    ----------
+        abbrvDict : dict
+            Dict containing lists of abbreviations for GEOSX command line options
+    """
+    def __init__(self):
+        self.abbrvDict = {"xml": ("--input", "-i"),
+                          "restart": ("--restart", "r"),
+                          "xpart": ("-x-partitions", "-x"),
+                          "ypart": ("-y-partitions", "-y"),
+                          "zpart": ("-z-partitions", "-z"),
+                          "non_blocking": ("--use-non-blocking", "-b"),
+                          "name": ("--name", "-n"),
+                          "supp_pinned": ("--suppress-pinned"),
+                          "outputdir": ("--output", "-o"),
+                          "timers": ("--timers", "-t"),
+                          "trace_data_mig": ("--trace-data-migration"),
+                          "pause_for": ("--pause-for")
+                         } 
+
+    def getAbbrv(self, optionName=None):
+        """
+        Returns the abbreviation corresponding to the requested option
+
+        Parameters
+        ----------
+            optionName : str
+                Name of the requested option
+
+        Returns
+        -------
+            str : Requested abbreviations
+        """
+        return self.abbrvDict[optionName][-1]
+
+
+    def getAllAbbrv(self, optionName=None):
+        """
+        Returns the abbreviation corresponding to the requested option
+
+        Parameters
+        ----------
+            optionName : str
+                Name of the requested option
+
+        Returns
+        -------
+            list of str : 
+                Requested abbreviations
+        """
+        try:
+            return self.abbrvDict[optionName]
+
+        except:
+            return [""]

pygeos-tools/src/geos/pygeos_tools/utilities/input/Xml.py

@@ -0,0 +1,120 @@
+# ------------------------------------------------------------------------------------------------------------
+# SPDX-License-Identifier: LGPL-2.1-only
+#
+# Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
+# Copyright (c) 2018-2024 TotalEnergies
+# Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
+# Copyright (c) 2023-2024 Chevron
+# Copyright (c) 2019-     GEOS/GEOSX Contributors
+# Copyright (c) 2019-     INRIA project-team Makutu 
+# All rights reserved
+#
+# See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+# ------------------------------------------------------------------------------------------------------------
+
+import os
+from xml.etree import cElementTree as ET
+import xmltodict
+from re import findall
+from ..mesh.InternalMesh import InternalMesh
+from ..mesh.VtkMesh import VTKMesh
+
+
+class XML():
+    def __init__(self, xmlFile):
+        self.filename = xmlFile
+
+        self.tree = ET.parse(xmlFile)
+        root = self.tree.getroot()
+        to_string  = ET.tostring(root, method='xml')
+
+        self.outputs = None
+
+        root = xmltodict.parse(to_string, attr_prefix="" ,dict_constructor=dict)
+        for k, v in root['Problem'].items():
+            words = findall('[A-Z][^A-Z]*', k)
+            words[0] = words[0].lower()
+            attr = ""
+            for word in words:
+                attr += word
+            setattr(self, attr, v)
+
+
+
+    def updateSolvers(self, solverName, **kwargs):
+        root = self.tree.getroot()
+        solver = root.find("./Solvers/"+solverName)
+        for k, v in kwargs.items():
+            if k in solver.attrib:
+                solver.set(k, v)
+                self.solvers[solverName].update({k:str(v)})
+
+
+    def updateMesh(self, **kwargs):
+        root = self.tree.getroot()
+        mesh = root.find("./Mesh//")
+        for k, v in kwargs.items():
+            if k in mesh.attrib:
+                mesh.set(k, v)
+                self.mesh[mesh.tag].update({k:str(v)})
+
+
+    def updateGeometry(self, boxname, **kwargs):
+        root = self.tree.getroot()
+        geometry = root.find("./Geometry//*[@name="+boxname+"]")
+
+        for i in len(self.geometry[geometry.tag]):
+            box = self.geometry[geometry.tag][i]
+            if boxname == box["name"]:
+                break
+
+        for k, v in kwargs.items():
+            if k in geometry.attrib:
+                geometry.set(k, v)
+                self.geometry[geometry.tag][i].update({k:str(v)})
+
+
+    def getMeshObject(self):
+
+        if "InternalMesh" in self.mesh.keys():
+            #Not working properly for now
+            return InternalMesh(self)
+
+        elif "VTKMesh" in self.mesh.keys():
+            vtkFile = self.mesh["VTKMesh"]["file"]
+            if not os.path.isabs(vtkFile):
+                vtkFile = os.path.join(os.path.split(self.filename)[0], vtkFile)
+            return VTKMesh(vtkFile)
+
+    def getAttribute(self, parentElement, attributeTag):
+        if parentElement == "root":
+            pElement = self.tree.find(f"./[@{attributeTag}]")
+        else:
+            pElement = self.tree.find(f"./*/{parentElement}/[@{attributeTag}]")
+
+        return pElement.get(attributeTag)
+
+
+    def getSolverType(self):
+        return [k for k in self.solvers.keys() if k[0].isupper()]
+
+
+    def getSourcesAndReceivers(self):
+        solverType = self.getSolverType()
+        if len(solverType) > 1:
+            pass
+        else:
+            src = self.getAttribute(f"{solverType[0]}", "sourceCoordinates")
+            src = eval(src.replace("{", "[").replace("}", "]"))
+
+            rcv = self.getAttribute(f"{solverType[0]}", "receiverCoordinates")
+            rcv = eval(rcv.replace("{", "[").replace("}", "]"))
+
+        return src, rcv
+
+
+    def exportToXml(self, filename=None):
+        if filename is None:
+            self.tree.write(self.filename)
+        else:
+            self.tree.write(filename)

pygeos-tools/src/geos/pygeos_tools/utilities/input/__init__.py

@@ -0,0 +1,18 @@
+# ------------------------------------------------------------------------------------------------------------
+# SPDX-License-Identifier: LGPL-2.1-only
+#
+# Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
+# Copyright (c) 2018-2024 TotalEnergies
+# Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
+# Copyright (c) 2023-2024 Chevron
+# Copyright (c) 2019-     GEOS/GEOSX Contributors
+# Copyright (c) 2019-     INRIA project-team Makutu 
+# All rights reserved
+#
+# See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+# ------------------------------------------------------------------------------------------------------------
+
+"""Input handle"""
+
+from .GeosxArgs import GeosxArgs, GeosxAbbrevOption
+from .Xml import XML